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carolindahms / TreeMix

Scripts to analyze data using TreeMix. This pipeline runs TreeMix with bootstrapping, helps choose number of migration events and creates a consensus tree. It plots the maximum likelihood tree with bootstrap values, drift and residuals and calculates statistics for every migration event, such as migration support, standard error and p-values.
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problem in step1 #1

Closed Yyeserin closed 2 years ago

Yyeserin commented 2 years ago

Hi!

I am trying to run the software in linux using the code below just for trial. I am sure that phylip exe works fine.

_sh ./Step1TreeMix.sh populations.treemix.gz 1 3 noRoot 3 /home/yeserin/snphylo/phylip-3.697/exe/consense 3spine 1 3 3

I keep getting the error pasted to the end.

I checked the line 49 in Step1_TreeMix.sh: __seq 1 $nboot | parallel -j$ncore dowork {} $infile $blockk $outname > $outname"_logfile_constree_bootrep.log"__

Is the problem related to the core usage, or something else?

I can provide more information if needed. I appreciate any help/suggestions a lot!

Best, Yeserin.

ERROR

_ Running TreeMix ./Step1_TreeMix.sh: line 49: parallel: command not found Running TreeMix: DONE gzip: bootstrap/3spine_constree_bootrep_1.treeout.gz: No such file or directory gzip: bootstrap/3spine_constree_bootrep_2.treeout.gz: No such file or directory gzip: bootstrap/3spine_constree_bootrep_3.treeout.gz: No such file or directory Bootstrap procedure: DONE Phylip - consensus tree construction: START Phylip - consensus tree construction: DONE Running TreeMix with consensus tree adding 1 to 3 migration edges ./Step1_TreeMix.sh: line 116: treemix: command not found ./Step1_TreeMix.sh: line 116: treemix: command not found ./Step1_TreeMix.sh: line 116: treemix: command not found ./Step1_TreeMix.sh: line 116: treemix: command not found ./Step1_TreeMix.sh: line 116: treemix: command not found ./Step1_TreeMix.sh: line 116: treemix: command not found ./Step1_TreeMix.sh: line 116: treemix: command not found ./Step1_TreeMix.sh: line 116: treemix: command not found ./Step1TreeMix.sh: line 116: treemix: command not found TreeMix - Bootstrap Analysis with migrations: DONE

Prashantevo commented 2 years ago

I think it is the problem with your parallel and treemix. provide a path as export PATH=$PATH:/home/directory/where/parallel/is and the same for the actual tree mix tool export PATH=$PATH:/home/directory/where/treemix/is. Then run step 1.

Yyeserin commented 2 years ago

Hi again,

My problem seems to be solved now after calling parallel and treemix packages. Thank for the advice!